net.sf.samtools.FileTruncatedException: Premature end of file

sourceforge.net | 5 months ago
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    SAM tools / Mailing Lists

    sourceforge.net | 5 months ago
    net.sf.samtools.FileTruncatedException: Premature end of file
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    GitHub comment 16#224552533

    GitHub | 6 months ago | royfrancis
    net.sf.samtools.FileTruncatedException: Premature end of file

    Root Cause Analysis

    1. net.sf.samtools.FileTruncatedException

      Premature end of file

      at net.sf.samtools.util.BlockCompressedInputStream.readBlock()
    2. picard
      BlockCompressedInputStream.read
      1. net.sf.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:290)
      2. net.sf.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:100)
      3. net.sf.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:169)
      3 frames
    3. Java RT
      DataInputStream.read
      1. java.io.DataInputStream.read(DataInputStream.java:132)
      1 frame
    4. picard
      MarkDuplicates.main
      1. net.sf.samtools.util.BinaryCodec.readBytesOrFewer(BinaryCodec.java:394)
      2. net.sf.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:371)
      3. net.sf.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:357)
      4. net.sf.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:182)
      5. net.sf.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:397)
      6. net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:373)
      7. net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:363)
      8. net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:330)
      9. net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:261)
      10. net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:112)
      11. net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:150)
      12. net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:96)
      12 frames